Implicit Solvent Model for Million-Atom Atomistic Simulations: Insights into the Organization of 30-nm Chromatin Fiber.

ABSTRACT: Molecular dynamics (MD) simulations based on the implicit solvent generalized Born (GB) models can provide significant computational advantages over the traditional explicit solvent simulations. However, the standard GB becomes prohibitively expensive for all-atom simulations of large structures; the model scales poorly, ∼n², with the number of solute atoms. Here we combine our recently developed optimal point charge approximation (OPCA) with the hierarchical charge partitioning (HCP) approximation to present an ∼n log n multiscale, yet fully atomistic, GB model (GB-HCPO). The HCP approximation exploits the natural organization of biomolecules (atoms, groups, chains, and complexes) to partition the structure into multiple hierarchical levels of components. OPCA approximates the

SUBMITTER: Izadi S 

PROVIDER: S-EPMC5649046 | biostudies-literature | 2016 Dec

REPOSITORIES: biostudies-literature